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ggonnella / gfapy

Gfapy: a flexible and extensible software library for handling sequence graphs in Python
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Compact the assembly graph [feature request] #9

Closed sjackman closed 3 years ago

sjackman commented 5 years ago

I'd like to compact the assembly graph (merge all possible segments). Bandage has this feature from the GUI, but doesn't expose it to the command line. See https://github.com/rrwick/Bandage/wiki/Editing-graphs#merge-all-possible-nodes

I'm currently interested in this feature for assembly graphs where all the overlap edges are blunt 0M, which makes merging the sequences trivial. This operation is also easy if the overlaps are perfect 1234M, but gets tricky if indels are involved. I'm not currently interested in handling indels.

ggonnella commented 3 years ago

I am sorry I did not answer properly to the feature request. Since I am cleaning up unfinished tasks I do it now, with only 2 and a half years delay. Sorry :( Actually a method already existed (I think also back then): merge_linear_paths(). I checked now with some tests that it also works with blunt ends (it does, correctly). Therefore I close the issue. Thank you, Shaun, and sorry again for the missing communication.